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Correspondence
geneyeo@ucsd.edu
In Brief
Interactions between stress granule
proteins exist ahead of a stress response
and candidate SG proteins modify
disease phenotypes in vivo.
Highlights
d APEX proximity labeling reveals 150 unknown SG proteins
in a dense protein network
*Correspondence: geneyeo@ucsd.edu
https://doi.org/10.1016/j.cell.2017.12.032
590 Cell 172, 590–604, January 25, 2018 ª 2017 Elsevier Inc.
SGs (Buchan et al., 2013; Jain et al., 2016; Ohn et al., 2008). (Figure S1C) to systematically identify three classes of G3BP1-
However, these efforts need to be complemented with in vivo interacting proteins in stressed and unstressed cells: (1) stress-
approaches that address potential loss or gain of SG protein independent interactors, which associate with G3BP1 indepen-
interactions following cell lysis. Furthermore, there is an unmet dently of stress; (2) stress-dependent partners, which associate
need to systematically examine the extent to which SG compo- with G3BP1 only under stress; and (3) stress-sensitive interac-
sition is dependent on cell type, the nature of the stressor, and tors, whose association with G3BP1 is lost or weakened during
the presence of disease-linked mutations in SG proteins. stress (Figure 1D).
In this study, we use a combination of ascorbate peroxidase To distinguish these interactors, we pursued four experi-
(APEX)-mediated in vivo proximity labeling (Rhee et al., 2013) mental schemes (Figure 1E). First, to identify stress-dependent
with quantitative mass spectrometry (MS) and an RBP-focused G3BP1 interactors, we characterized biotinylated proteins
immunofluorescence (IF) approach to comprehensively and in stressed versus unstressed G3BP1-APEX2-GFP cells
significantly expand the repertoire of known SG proteins across (experiment 1). Next, we compared lysates from stressed
different cell types, stress conditions, and disease states. We G3BP1-APEX2-GFP cells incubated with BP to lysates of
show that SG proteins form a dense protein interaction network identically treated cells for which the BP substrate was
(PIN) in unstressed cells that is poised to enable rapid SG omitted (experiment 2). Third, to control for diffuse cytoplasmic
assembly in response to stress. In addition, we find that SGs in labeling by G3BP1-APEX2-GFP, we also compared lysates
neuronal cells are particularly diverse in composition and contain from stressed G3BP1-APEX2-GFP and NES-APEX2-GFP cells
numerous protein quality control (PQC) factors. We reveal aber- (experiment 3). Last, to define stress-independent as well as
rant composition, behavior, and subcellular localization of SGs stress-sensitive G3BP1 interactors, we profiled lysates from
in motor neurons derived from stem cell models harboring unstressed G3BP1-APEX2-GFP and NES-APEX2-GFP cells
ALS-associated mutations in HNRNPA2B1 and C9orf72. By sys- (experiment 4). For each approach, we conducted biologically
tematically integrating our refined SG proteome with published independent triplicate labeling reactions followed by mixing of
neurodegeneration-relevant datasets, we provide a framework lysates and streptavidin purification of biotinylated proteins.
for further investigations into the molecular underpinnings of Affinity-purified samples and the corresponding input samples
SG biology and how it relates to human disease. To underscore were analyzed by quantitative MS. In total, we detected 1,416
the potential of identifying unexpected disease-relevant factors proteins across all input samples and 2,020 proteins across
among SG proteins, we show that known and previously all streptavidin enrichments (Figure S1D), accounting for 64%
unknown SG components modify neurotoxicity in Drosophila (153) of a manually curated list of 238 annotated SG proteins
models of FUS-, TDP-43-, and C9orf72-mediated degeneration. (Table S2). Protein identification and quantification of heavy to
We characterize one of these, UBAP2L, as an essential, disor- light (H/L) ratios were highly reproducible across replicate ex-
dered, and highly aggregation-prone SG protein that can modu- periments (Figure S2; Table S1). We compared the enrichment
late ALS phenotypes in vivo. of known SG proteins to the background distribution of all
detected proteins (Figures 1E and 2A). Known SG proteins
RESULTS were significantly enriched across all four approaches, with
the greatest shift in log2 H/L ratios detected in experiments
Endogenously Tagged G3BP1-APEX2-GFP Allows for 2 and 3. Interestingly, we observed attenuated enrichment of
Specific Biotin Labeling of SG Proteins known SG proteins in experiment 1 and that even in the
To investigate the protein composition of SGs in living cells, we absence of stress (experiment 4), known SG proteins appeared
performed proximity labeling using an engineered ascorbate to be enriched in the IP samples (Figures 1E and 2A).
peroxidase (APEX2) fused to the well-characterized SG protein
G3BP1 (Figure 1A). We used CRISPR/Cas9-directed genome G3BP1-APEX2-Mediated Biotinylation Identifies SG
engineering to insert APEX2-GFP into the endogenous G3BP1 Proteins with High Specificity
locus in HEK293T cells (Figure S1A). The resulting G3BP1- We used a series of analysis steps to identify candidate SG pro-
APEX2-GFP fusion protein allows visualization of SGs upon teins from our quantitative proteomics data (Figure S1E). We first
sodium arsenite (NaAsO2) exposure, as well as robust and rapid leveraged our curated list of annotated SG proteins to determine
biotin labeling of SG proteins in the presence of biotin-phenol log2 H/L ratio cutoffs in a non-parametric approach similar to
(BP) and hydrogen peroxide (H2O2) (Figures 1B and 1C). As a previous ratiometric SILAC APEX experiments (Hung et al.,
specificity control, cells with constitutive expression of cyto- 2014). We ranked identified proteins in each replicate by their
plasmic-localized APEX2 (NES-APEX2-GFP) (Figure S1B) show log2 H/L ratio and calculated the frequency distribution of known
a diffuse GFP signal and a biotinylation pattern that is unaffected SG proteins across the ranked lists (Figure 2A). We chose as a
by NaAsO2 (Figures 1B and 1C). conservative cutoff the ratio at which the frequency of known
SG proteins in a moving window fell below 2-fold the frequency
Identification of Stress-Dependent and Independent SG across all detected proteins. In parallel, we applied an empirical
Proteomes Using Quantitative Proteomics Bayes method (Kammers et al., 2015) to identify proteins that
Since G3BP1 is essential for SG formation and robustly localizes were significantly enriched in heavy over light samples. This
to SGs, we reasoned that defining the interactome proximal to method is based on the linear models for microarray data
G3BP1 under stress conditions approximates the SG proteome. (LIMMA) approach (Smyth, 2004), which is also applicable to
We employed a series of quantitative proteomics experiments quantitative proteomics data (Margolin et al., 2009). It uses the
actual observed data to moderate individual protein variances by # in Figure 2B). Table S3 provides a detailed overview of
through an estimated global sample variance, and thus enables all hit candidates across all four experimental designs.
a more robust identification of significant changes in protein Underscoring the robustness of the approach, many well-
abundance than ordinary t-statistics. The resulting moderated characterized SG proteins (e.g., G3BP1, TIA1, CAPRIN1,
p values are corrected for multiple hypothesis testing using PABPC1, FMR1, and ATXN2) were identified as highly significant
a modified Benjamini-Hochberg false discovery rate (FDR) interactors across multiple experiments (Figure 2C). In summary,
approach to determine a moderated q-value (q.mod). nearly 80% (96/123) of hits are known SG proteins (69/123), were
For the final list of SG candidates, we initially selected all verified by IF (13/123), or have additional data supporting SG as-
proteins that were above the ratio cutoff in at least 2 out of 3 sociation, such as closely related family members or interactions
IP replicates. We defined a set of 123 proteins from the with known SG proteins (14/100; e.g., HNRNPDL, YTHDF3). For
overlapping sets as shown in Figure 2B (shaded in gray). Of example, the DEAD-box helicase DDX1 is known to localize to
these, 80% (99/123) are also statistically significantly enriched SGs and was shown to form an RNA transport complex with
(q.mod < 0.05) in at least one experiment. For most of the re- C14ORF166, FAM98A/B, and RTCB (Pérez-González et al.,
maining 24 proteins, no significance values could be deter- 2014), all of which we identify as SG candidates (Figures 2B
mined due to missing data in one of the biological replicates. and 2C). Interestingly, our SG protein set also contains
However, as 25% of these proteins were previously known ANXA11, its closest paralog ANXA7, and their interactor PEF1
SG proteins, we chose to retain them in our final list (marked (Figures 2B and 2C). While none of these proteins had previously
HeLa cells to either NaAsO2 or heat shock (30 min at 42 C) and screens in three different cell types (HepG2, HeLa, and NPCs)
performed a screen with our RBP antibody collection. Of the 313 treated with NaAsO2. We identified a total of 77 SG-RBPs, with
RBP antibodies tested, 17% (52 RBPs) localized to SGs. Among over half of these (42/77) localizing to SGs in all three cell types
these, 77% (40/52) localized to SGs under both stress condi- and the remaining 35/77 proteins exhibiting varying degrees of
tions, while 23% (12/52) exhibited stress-type-specific SG tar- cell-type specificity (Figures 4E–4G; Table S5). For example,
geting (Figures 4B–4D; Table S5). For example, UBAP2L robustly UBAP2L co-localized with SGs in all cell types, while SRSF9,
localized to SGs in both stress conditions, while SG-association EIF3A and SRP68 were selectively targeted to SGs in HepG2
of NOLC1 and SF1 was specific to NaAsO2 or heat shock, cells, HeLa cells, or NPCs, respectively (Figures 4E and 4G).
respectively (Figures 4B and 4D). We next conducted parallel Notably, consistent with our APEX results, we found that about
bottom panels represent zoomed-in views of the indicated selection separately showing TIA-1 (red) or the test RBP (green). Arrowheads indicate examples
of RBPs co-localized with TIA-1.
(F) Venn diagram comparing SG proteins in HepG2, HeLa and NPCs treated with NaAsO2.
(G) Mean granule penetrance of proteins with either cell-type-independent or cell-type-specific SG localization.
Scale bars in (B) and (E), 20 mm. Error bars in (D) and (G) represent SD. See also Table S5.
In addition to providing a resource of nearly 150 previously appear to form de novo in response to stress, their emergence
unknown candidate SG proteins for further validation, our study represents a moderate and transient shift in a tightly controlled
links many known and previously unidentified SG proteins to equilibrium of protein-protein and protein-RNA interactions
human disease and provides unexpected and exciting insights (Figure 7A). Allocating high local concentrations of processing
into SG biology and how it relates to neurodegeneration (Fig- factors and substrates into interconnected RNP assemblies
ure 7). First, our SG-APEX data in stressed and unstressed cells, enables highly efficient processing to take place but at the
combined with independent PPI data, show that much of the same time increases the risk of uncontrolled protein aggregation.
underlying network of SG protein interactions already exists in As a result, cells have evolved mechanisms for efficiently
unstressed cells. This finding sharpens the picture of a highly resolving transient higher-order RNP assemblies, especially in
evolved and dense network of RNPs that integrates the many the context of a temporary stress response. Our results highlight
steps of gene expression regulation. As a result, although SGs how SG proteins are tightly integrated with PQC pathways, most
Further information and requests for resources and reagents should be directed to and will be fulfilled by the Lead Contact,
Gene W. Yeo (geneyeo@ucsd.edu). Important plasmids described in this study will be deposited in the Addgene plasmid respository
and available under a standard MTA.
Immortalized human cell lines and human pluripotent stem cells (hiPSCs) were utilized in this study. The Lenti-X HEK293T cell line is
derived from human female tissue, the HepG2 cell line is derived from human male hepatocellular carcinoma tissue and HeLa S3 cells
are derived from human female cervical adenocarcinoma tissue. HEK293T and HeLa cells were maintained in DMEM and HepG2
cells in Hyclone growth medium both supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37 C in a humid-
ified incubator under 5% CO2. hiPSCs were maintained under feeder-free conditions in mTeSR1 medium (Stem Cell Technologies)
and propagated either by single-cell passaging using Accutase or clump-passaging using enzyme-free dissociation buffer (EDTA).
Flies were reared on standard yeast-agar-cornmeal medium and crosses were performed at 25 C. The degenerative eye phenotype
was assessed two weeks after the crosses were performed, while the wing margin notching phenotype was scored in 3-5 days old
adult flies of the F1 generation.
METHOD DETAILS
APEX-mediated biotinylation
HEK293Ts and NPCs were grown in heavy or light SILAC medium for at least 5 passages prior to APEX labeling and isotope label
incorporation efficiency was confirmed to be above 98%. Cells were seeded in 10cm culture dishes one day prior to labeling to
be 80% confluent the following day and either left unstressed or treated with either 250mM (NPCs) or 500mM (HEK293T) NaAsO2
or 500nM thapsigargin for 1h at 37 C. 500mM biotin-phenol (BP) was added to the medium at the same time as stressors except for
the no-substrate control samples. APEX labeling was performed by adding hydrogen peroxide to a final concentration of 1mM for
60 s before quenching the biotinylation reaction by adding Trolox ((+/ )-6-Hydroxy-2,5,7,8-tetramethylchromane-2-carboxylic
acid, Sigma 238813) and sodium L-ascorbate (Sigma A4034) to a final concentration of 5 and 10mM, respectively. Samples were
washed once with cold PBS, collected using cell scrapers, pelleted for 3min at 300 g and immediately suspended in cold lysis buffer
(8M urea, 150mM NaCl, 20mM Tris-HCl pH 8.0, Protease Inhibitor Cocktail Set III, EDTA-Free (EMD Millipore, cat no. 539134), 5mM
Trolox and 10mM sodium L-ascorbate). Samples were sonicated and cleared by centrifugation at 12000rpm for 10min at 4 C. Protein
concentration was determined using by 660nm protein assay (Pierce, PI22660) and equal amounts of protein from corresponding
light and heavy labeled samples were mixed for a total of 2-4mg of protein. Samples were diluted to 2M urea by adding 3 volumes
of 150mM NaCl, 20mM TrisHCl pH 8.0 with protease inhibitors and quenchers. For affinity purification, 100ul of streptavidin mag-
netic beads (Pierce, PI88817) were washed once in 2M urea buffer, resuspended directly in the sample, incubated for 2h at room
temperature and washed 8 times in 2M urea buffer. Following the washes, beads were centrifuged at 240 RCF for 5 min at 4 C.
The supernatant was removed and a volume of 50mM Ammonium bicarbonate buffer equal to the volume of the beads was added.
For the on-bead digestion of the IP samples, the ammonium bicarbonate buffer was removed and replaced with an equal volume of
20mM Tris pH8.0 with endoproteinase Lys-C (Wako) at a 1:100 (w/w) enzyme substrate ratio. Samples were incubated for 1hr at
37 C. Following the Lys-C digestion, CaCl2 was added to a final concentration of 1mM along with 500ng sequencing grade trypsin
(Promega). The corresponding input samples for each IP were diluted to a final urea concentration of 1M using 50mM Ammonium
bicarbonate. Lys-C digestion was done as described above for the IP samples followed by trypsin digestion with a 1:100 (enzyme:
protein) ratio After trypsin addition, all samples were incubated at 37 C for overnight with agitation. After the digestion, an equal
volume of 5% formic acid was added to the digestion mixture and incubated at room temperature for 10 minutes. The supernatant
was transferred to a new 1.5mL tube and the elution step was repeated one more time. The trypsin-digested input and IP samples
were concentrated and desalted using the Stage-Tip method and reconstituted in a 5% Formic acid/5% acetonitrile for MS analysis.
Drosophila genetics
Flies were reared on standard yeast-agar-cornmeal medium and crosses were performed at 25 C. Drosophila transgenic
strains carrying GAL4 inducible human ALS disease causing alleles of FUS/TLS and TDP-43 were previously described
(Lanson et al., 2011; Ritson et al., 2010). Standard genetic procedures were used to generated the GMR-GAL4/CyO, tub-GAL80;
UAS-FUS-hR521C/TM6B, Tb and GMR-GAL4, UAS-TDP-43-hM337V/CyO, tub-GAL80 transgenic strains (Periz et al., 2015).
Drosophila strains containing the Exelixis insertional disruptions are publically available from the Department of Cell Biology, Harvard
Medical School include Rox8e04432, Rbp6d08411, ligf03269, CG2889d07154, D12e01238, Su(var)205c06825 and shepd07053. The dominant
effect of the introduction of these inserts on degenerative eye phenotypes of GMR-GAL4; UAS-FUS-hR521C and GMR-GAL4,
UAS-TDP-43-hM337V was assessed two weeks after the crosses were performed. Qualitative changes in pigmentation, ommatidial
structure and glossiness phenotypes were monitored for enhancement or suppression.
UAS-(GR)80 transgenic fly lines were generated previously (Yang et al., 2015). Vg-Gal4/Cyo; UAS-(GR)80/TM6B flies were crossed
with individual genetic mutant or UAS-RNAi lines for a specific gene, which were obtained from the Bloomington Drosophila Stock
Center. For crosses with genetic mutant alleles, w1118 flies were used as the control. For crosses with UAS-RNAi lines, UAS-GFP
served as the control. After the cross, 3-5 days old adult flies of the F1 generation were scored under the dissecting microscope.
The number of flies with or without the wing margin notching phenotype was counted.
Image analysis
MetaXpress v3.1 software was used for all image analysis and quantifications were carried out using an in-house script
(see Methods S1).
The accession number for the proteomics data reported in this paper is MassIVE MS data repository (https://massive.ucsd.edu/
ProteoSAFe/static/massive.jsp): MSV000081554.
Figure S1. APEX Cell Line Generation, MS Experimental Design, and Data and Analysis, Related to Figure 1
(A) Schematic of CRISPR-Cas9-mediated endogenous tagging of the G3BP1 locus.
(B) Schematic of generating a constitutive hPGK::NES-APEX2-GFP-expressing HEK293T cell line.
(C) Schematic description of the SILAC experimental workflow.
(D) Venn diagram showing overview of all proteins detected by MS in streptavidin affinity-purified samples, corresponding input samples in relation to a list of
known SG proteins.
(E) Flow chart depicting data analysis steps to identify candidate SG proteins.
Figure S2. Reproducibility of Protein Identification and Quantitation across Replicates, Related to Figure 1
(A) Venn diagrams showing overlap between proteins identified from HEK293T cells in biological replicate experiments.
(B) Scatterplots showing correlation between log2 H/L ratios for identified proteins from biological replicate experiments.
Figure S3. APEX-Mediated Biotinylation, Experimental Design, and Detected Proteins in Neural Progenitor Cells, Related to Figure 3
(A) Streptavidin staining of unstressed (top panel) and sodium arsenite-treated (middle and bottom panels) CV-B G3BP1-APEX2-GFP neural progenitor cells.
Cells were either incubated in the presence (upper and middle panels) or absence (lower panel) of biotin phenol.
(B) SG-APEX experimental designs used in NPCs.
(C) Venn diagram showing overview of all proteins detected by MS in NPC input and IP samples and overlap with known SG proteins.
(D) Venn diagram showing overlap of all proteins detected above fold-change cutoff in NPC stressed with either sodium arsenite or thapsigargin.
Figure S4. Expression of Cell-Type-Specific Markers and Neurite-Localized Granules in iPSC-Derived Motor Neurons, Related to Figure 5
(A) IF staining of wild-type and HNRNPA2B1 mutant motor neurons showing expression of the motor neuron-specific phosphorylated neurofilament SMI-31 and
the transcription factor ISL1/2.
(B) IF staining of wild-type and HNRNPA2B1 mutant motor neurons that were either left untreated or stressed with puromycin, then co-labeled with G3BP1 (green)
and a panel of RBP antibodies (red). Upper panels are merged views with lower resolution. In each panel, the indicated insets at the bottom are zoomed views of
the same field showing G3BP1 (green) and the RBP (red).
(C) Enrichment analysis for KEGG pathways and Biological Process Gene Ontology term as determined by the Enrichr gene enrichment analysis tool.
Figure S5. Extended Dataset Cross-Comparison, Additional Fly Modifiers, UBAP2L Protein Structure and Co-localization with Stress
Granule Proteins, Related to Figure 6
(A) Venn diagram showing overlap between SG proteins identified in our study, compared to the SG core proteome (Jain et al., 2016) and known SG proteins.
(B) Heatmap for all 1312 proteins represented across selected SG and neurodegeneration-relevant datasets, indicating whether a protein is present (blue box) or
absent (white box) from each dataset. Proteins are ranked by the number of datasets they are part of in descending order from top to bottom.
(C) Quantitation of the wing notching phenotype caused by poly(GR) toxicity in flies. w1118 flies were used as the control for genetic mutant alleles, while UAS-GFP
served as the control for different UAS-RNAi lines. The Bloomington stock numbers for each mutant or RNAi line are listed.